I am using git flow, but I think documentation should track the master branch, rather than develop. It does work with develop, but I would think that I should be able to specify master too, which seems to not work.

Well, there is a master branch on GitHub. I'm not sure if there's anything to do on my end, but I use git flow on all of my projects, and haven't seen problems elsewhere, but I added them all some time ago. I was just trying to update this project, but found it wasn't in Rubydoc.info, although it certainly was before.